SNP_Utils

SNP_Utils is a Python program that creates a VCF file for a list of SNPs given in an Illumina lookup table. There are three subroutines for SNP_Utils: CONFIG, BLAST, and SAM

To get basic usage information, simply run the program without any arguments

$ ./snp_utils.py
usage: snp_utils.py [-h] {CONFIG,BLAST,SAM} ...

optional arguments:
  -h, --help          show this help message and exit

Subroutine:
  Choose a subroutine

  {CONFIG,BLAST,SAM}  'BLAST' means we are running a BLAST search to find
                      SNPs, 'SAM' means we are using a SAM file, 'CONFIG' is
                      used to configure a BLAST search

More detailed information can be found for each subroutine by passing the name of the subroutine and the -h | --help flag or by reading below

Illumina Lookup Table

The Illumina lookup table is a two-column, headerless table that has a SNP ID and contextual sequence in with the SNP in brackets ([A/B]) shwogin the two states for the SNP (A and B). The two columns are tab-delimited.

Example

SNP_1   ACGTCACGATCGA[A/G]ACGTATGCGAAGTTCGCC
SNP_2   GCTAGACTACCAG[G/T]GTCACGATGCCGTCAGTC

`CONFIG`

The CONFIG subroutine is used only when running BLAST within SNP_Utils. This step is required before running BLAST, but not required before parsing a BLAST XML file. Options for CONFIG are as follows:

Choosing whether the reference is in FASTA or nucleotide BLAST database format and specifying the path to these files
E-value threshold
Maximum number of hits and hsps
Percent identity to keep
Whether or not to keep the FASTA file generated from the Illumina lookup table

The configuration file is written in INI format

`BLAST`

The BLAST subroutine is used to run and parse BLAST results to create a VCF file of SNPs from an Illumina lookup table. To run BLASTn within SNP_Utils, you must configure using the CONFIG subroutine. BLAST can also rank SNPs; high-ranking SNPs are those that had a low e-value and high bit-score in BLAST. When ranking, only the highest hit for every SNP is kept, ties for highest include both SNPs. To parse a previously-generated BLAST XML file, you do not need to configure BLAST. Options for BLAST are as follows:

Choosing either a BLAST config or XML file as input
Setting the basename for the output
Choosing whether or not we rank SNPs
Setting filtering schemes to eliminate duplicate SNPs

`SAM`

The SAM subroutine is used to parse a SAM file designed around the Illumina lookup table. This SAM file should be generated by read-mapping the Illumina lookup sequences to a reference genome. Options for SAM are as follows:

Choosing the SAM file and reference genome in FASTA format
Setting the basename for the output
Setting filtering schemes to eliminate duplicate SNPs

Filtering Final VCF

SNP_Utils can filter found SNPs in an attempt to remove duplicate positions. Filtering works with both BLAST and SAM subroutines. The following filtering schemes are available:

Use a genetic map to keeps SNPs on the chromosome specified by the map. Use -b | --by-chrom and -m | --genetic-map to filter by chromosome
Set a minimum distance threshold in base pairs and keep the leftmost SNP when two are closer than this threshold. Use -t | --threshold to specify this distance in base pairs
Use genetic map distances to choose the SNP closest to this position proportionally. This option ignores SNPs on other chromosomes. Please note that if using the BLAST subroutine, this filtering scheme requires that a reference sequence be used instead of a BLAST database or that the BLAST database was generated with the -parse_seqids flag toggled. Use -d | --by-distance and -m | --genetic-map to filter by genetic map distance

Outputs

SNP_Utils creates between one and six output files

File name	Contents
config.ini	BLAST configuration file generated from `CONFIG`
fasta_database.xml	XML results from running BLAST with SNP_Utils, generated from `BLAST`
lookup.fasta	Lookup table in FASTA format for running BLAST with SNP_Utils, generated from `BLAST` and `CONFIG` with `-k
output.vcf	VCF file with confident SNP positions, generated from `BLAST` and `SAM`
output_masked.vcf	VCF file with masked ('N') alternate states for each SNP, these are SNPs that we could not find a position for given the Illumina lookup table, generated from `BLAST` and `SAM` if there were masked SNPs
output_failed.log	List of SNP IDs that we could not find at all, generated from `BLAST` and `SNP` if there were failures

Dependencies

SNP_Utils depends on the following:

The last four all available on PyPi and can be downloaded using pip3 (included with Python 3.4 or greater)

mojaveazure / SNP_Utils